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The bovine lactation genome: insights into the evolution of mammalian milk

Danielle G Lemay1*, David J Lynn2, William F Martin1, Margaret C Neville3, Theresa M Casey4, Gonzalo Rincon5, Evgenia V Kriventseva6, Wesley C Barris7, Angie S Hinrichs8, Adrian J Molenaar9, Katherine S Pollard10, Nauman J Maqbool11, Kuljeet Singh9, Regan Murney9, Evgeny M Zdobnov121314, Ross L Tellam7, Juan F Medrano5, J Bruce German115 and Monique Rijnkels16

Author Affiliations

1 Department of Food Science and Technology, University of California Davis, One Shields Avenue, Davis, CA 95616, USA

2 Department of Molecular Biology and Biochemistry, Simon Fraser University, University Drive, Burnaby, BC, V5A 1S6, Canada

3 Department of Physiology and Biophysics, University of Colorado Denver, Anschutz Medical Center, E. 19th Ave, Aurora CO 80045, USA

4 Department of Animal Science, Michigan State University, East Lansing, MI 48824-1225, USA

5 Department of Animal Science, University of California Davis, One Shields Avenue, Davis, CA 95616, USA

6 Department of Structural Biology and Bioinformatics, University of Geneva Medical School, rue Michel-Servet, 1211 Geneva, Switzerland

7 CSIRO Livestock Industries, Queensland Bioscience Precinct, Carmody Road, St Lucia, Queensland 4067, Australia

8 Center for Biomolecular Science and Engineering, University of California Santa Cruz, High St, Santa Cruz, CA 95064, USA

9 Dairy Science and Technology, AgResearch, Ruakura Research Centre, East Street, Hamilton, 3240, New Zealand

10 Division of Biostatistics and Gladstone Institutes, University of California San Francisco, Owens St, San Francisco, CA 94158, USA

11 Bioinformatics, Mathematics and Statistics, AgResearch, Invermay Agricultural Centre, Puddle Alley, Mosgiel 9053, New Zealand

12 Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet, 1211 Geneva, Switzerland

13 Swiss Institute of Bioinformatics, rue Michel-Servet, 1211 Geneva, Switzerland

14 Imperial College London, South Kensington Campus, London, SW7 2AZ, UK

15 Nestlé Research Centre, Vers-chez-les-Blanc CH-1000, Lausanne 26, Switzerland

16 Department of Pediatrics, Children's Nutrition Research Center, Baylor College of Medicine, Bates Street, Houston TX 77030, USA

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Genome Biology 2009, 10:R43  doi:10.1186/gb-2009-10-4-r43

Published: 24 April 2009

Additional files

Additional data file 1:

Milk and mammary gene sets.

Format: XLS Size: 1.7MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional data file 2:

Custom track in BED format for the UCSC Genome Browser, bovine assembly 3.1.

Format: BED Size: 34KB Download file

Open Data

Additional data file 3:

Custom track in BED format for the UCSC Genome Browser, bovine assembly 3.1.

Format: BED Size: 632KB Download file

Open Data

Additional data file 4:

Custom track in BED format for the UCSC Genome Browser, bovine assembly 3.1.

Format: BED Size: 212KB Download file

Open Data

Additional data file 5:

Custom track in BED format for the UCSC Genome Browser, bovine assembly 3.1.

Format: BED Size: 480KB Download file

Open Data

Additional data file 6:

Custom track in BED format for the UCSC Genome Browser, bovine assembly 3.1.

Format: BED Size: 148KB Download file

Open Data

Additional data file 7:

Custom track in BED format for the UCSC Genome Browser, bovine assembly 3.1.

Format: BED Size: 124KB Download file

Open Data

Additional data file 8:

Genomic locations of curated milk trait QTL

Format: XLS Size: 49KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional data file 9:

Custom track in BED format for the UCSC Genome Browser, bovine assembly 3.1.

Format: BED Size: 19KB Download file

Open Data

Additional data file 10:

Additional analysis and discussion of milk trait QTL density

Format: DOC Size: 55KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional data file 11:

Candidate genes that occur within QTL with one spreadsheet per milk trait

Format: XLS Size: 591KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional data file 12:

Custom track in BED format for the UCSC Genome Browser, bovine assembly 3.1.

Format: BED Size: 67KB Download file

Open Data

Additional data file 13:

Custom track in BED format for the UCSC Genome Browser, bovine assembly 3.1.

Format: BED Size: 83KB Download file

Open Data

Additional data file 14:

Custom track in BED format for the UCSC Genome Browser, bovine assembly 3.1.

Format: BED Size: 107KB Download file

Open Data

Additional data file 15:

Custom track in BED format for the UCSC Genome Browser, bovine assembly 3.1.

Format: BED Size: 178KB Download file

Open Data

Additional data file 16:

Custom track in BED format for the UCSC Genome Browser, bovine assembly 3.1.

Format: BED Size: 117KB Download file

Open Data

Additional data file 17:

Significant genomic clusters within each milk and mammary gene set

Format: XLS Size: 174KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional data file 18:

Custom track in BED format for the UCSC Genome Browser, bovine assembly 3.1.

Format: BED Size: 10KB Download file

Open Data

Additional data file 19:

Accession numbers of mammalian orthologs of bovine milk protein genes

Format: XLS Size: 173KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional data file 20:

More detail on the conservation of milk protein genes in mammals

Format: DOC Size: 54KB Download file

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Open Data

Additional data file 21:

EST libraries that were surveyed for this study, the number of ESTs in each library, a description of the physiological state of the animal and tissue used to derive the library, and, if the library was excluded from this study, the reason for exclusion.

Format: XLS Size: 20KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional data file 22:

Methods used to probe relative mRNA levels of LGB-II, PCYOX1, and ART4 in bovine mammary tissue at different stages of development and the RT-PCR results.

Format: DOC Size: 104KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data